My guess is the oil pump gear is indexed slightly different than the old one, or the gear was worn on the old one to the point of changing the static timing when the new one was installed. The distributor has more timing adjustment than it appears. There are two adjustment bolts, one easily seen and another on the bottom, hex head down threads point up thru a plate. The plate on the underside of the distributor is adjustable, it may just be a matter of loosening the bolt on the underside and reset with the timing where needed and lock it down.
For the knocking sound - my guess is you will find a rod bearing or bearings that are worn.